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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgttgcagtaaaacagttttatttaaaaacttgtaacctggaaagagatatgtaactgtgtatttggtcttataatatatagATTCTGCAAGAGGAAATTGGTGGCGTGAAAGGTCATTTTGGACCTATTAATGCTTTGGCATTCAGTCCTGATGGGAAGAG

Basic information

species Arabidopsis thaliana
transcript AT2G46290.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os08g21660.2 (Oryza sativa), 3'ss of exon 5
-------------------------gttagtgttgcagt-aaaacagtt-ttatttaaaaacttgt---aacctggaaagagatatgtaactgtgtatttggtcttataatatatagATTCTGCAAGAGGAAATTGGTGGCGTGAAAGGTCATTTTGGACCTATTAATGCTTTGGCATTCAGTCCTGATGGGAAGAG
                           |  ||||  ||| | |||| |  |  | |    |  | |   ||  |  |    | | |  ||   ||    |  | |  |  | | |||||| ||||||||||||||||||| || ||||| ||||||||||| ||||| ||  ||||||| | ||||||||||  |||
gtcagttcttcgcacatagtttccatcttatgttttagtgagaacaatgatcgtgtggttatcttttcaaagttatattttgctgttcaagaatgagagttctatatttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG

upper sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os05g16660.1 (Oryza sativa), 3'ss of exon 5
-------------------------------------gttagtgttgcagtaaaacagttttatttaaaaac-ttgtaacctggaa-agagatatgtaactgtgtatttggtcttataatatatagATTCTGCAAGAGGAAATTGGTGGCGTGAAAGGTCATTTTGGACCTATTAATGCTTTGGCATTCAGTCCTGATGGGAAGAG
                                     || ||        ||    |||||| |||   ||  || |    | |   ||  ||| |  ||| | |||||    ||         ||||| ||||||||||||||||||| || ||||| ||||||||||| ||||| ||  ||||||| | |||||||||   |||
gtcagttctttgcacatggtttctatcttatgttttagtgagaacaatgatagtgtagttttcttttgcaatgttattttttcgtttagcaataagacact-tatattttacttt--------cagATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAG

upper sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G143330_T01 (Zea mays), 3'ss of exon 5
----------------------gttagtgttgcagtaaaacagtttta----tttaaaaacttgtaacctggaaagagatatgtaactgtgtatttggtcttataatatatagATTCTGCAAGAGGAAATTGGTGGCGTGAAAGGTCATTTTGGACCTATTAATGCTTTGGCATTCAGTCCTGATGGGAAGAG
                       | | ||    | |      || |||    ||   ||  ||| |  ||   || |  |     | | | ||||    |||    | | |||||| ||||||||||||||||||| || ||||| |||||||| || ||||||||||||||||| | ||||||||||  |||
gtgatttttcagttcacagaatataaatgccttactctttttgtgttacatcttgctaactttgcatgcttacaatatttgaaccattat-tattaaaacttgctcttt-tagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG

upper sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G028834_T03 (Zea mays), 3'ss of exon 5
---------------gttagtgttgcagtaaaacag------ttttat-ttaaaaacttg-taacctggaa-----agagatatgtaactgtgt--atttggtcttataatatat-agATTCTGCAAGAGGAAATTGGTGGCGTGAAAGGTCATTTTGGACCTATTAATGCTTTGGCATTCAGTCCTGATGGGAAGAG
               |||| |     |  ||  ||       |||| | |||    |||| |||| ||| |     | |  | |  ||||||    |||    |||    | | | ||||| ||||||||||||||||||| || ||||| |||||||| || ||||||||||||||||| | ||||||||||  |||
gtaatttctttttcagttaataaattatcaaggcattactccttttgtgttacttccttgctaacttggtatacttacaatttttgaactgttctgattaaaacttgctctcttttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGACATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG

upper sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA12G00510.1 (Glycine max), 3'ss of exon 3
---------gttagtgttgcagtaaaacagttttatttaaaaacttgtaacctggaaag---agatatgtaactgtgtatttggtcttataatatatagATTCTGCAAGAGGAAATTGGTGGCGTGAAAGGTCATTTTGGACCTATTAATGCTTTGGCATTCAGTCCTGATGGGAAGAG
          ||  | ||      | ||  | || | ||     |  | |  | ||| |   |  ||| |  ||   | |||  | | ||   || |||||||| ||||| |||||||| || |||||||| ||||||||||| |||||||| ||||| || |  |||||||| || ||
gtaagtttgtttgcttttcttcctagactatgttgtgtactg--tgatgatattgaatgtctacttattttgcttccttttttttttcatttgat-tagATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

upper sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA01G03610.1 (Glycine max), 3'ss of exon 6
----------gttagtgttgcagtaaaacagtt--ttatttaaaaacttgtaacctgga---aagagatatgtaactgtgtatttggtcttataatatatagATTCTGCAAGAGGAAATTGGTGGCGTGAAAGGTCATTTTGGACCTATTAATGCTTTGGCATTCAGTCCTGATGGGAAGAG
           ||  | || |  ||  |   ||  || | |||  |  |||||| |  |   |       | | | |   |||||| | ||    |   |||||||| ||||| |||||||| || || ||||| ||||||||||| |||||||| ||||| || |  |||||||| || ||
gtaagttttttttttttttcctttactatgtttagttctctaatgatatgtaacatctacttattttgctttttatttcatatttgttattcatttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

upper sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA01G03610.2 (Glycine max), 3'ss of exon 6
------gttagtgttgcagtaaaacagtt--ttatttaaaaacttgtaacctggaaagagata---tgtaactgtgtatttggtcttataatatatagATTCTGCAAGAGGAAATTGGTGGCGTGAAAGGTCATTTTGGACCTATTAATGCTTTGGCATTCAGTCCTGATGGGAAGAG
       ||  | || |  ||  |   ||  || | |||  |  |||||| |  |   |  |    | | | |   |||||| | ||    |   |||||||| ||||| |||||||| || || ||||| ||||||||||| |||||||| ||||| || |  |||||||| || ||
gttttttttttttttcctttactatgtttagttctctaatgatatgtaacatctacttattttgctttttatttcatatttgttattcatttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

upper sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv01s0011g06630.t01 (Vitis vinifera), 3'ss of exon 6
---gttagtgttgcagtaaaacagttt-tatttaaaaacttgtaacctggaaagagatatgtaactgtgta---tttggtcttataatatat-agATTCTGCAAGAGGAAATTGGTGGCGTGAAAGGTCATTTTGGACCTATTAATGCTTTGGCATTCAGTCCTGATGGGAAGAG
    |   | |     || | | || | | | |       |||    || |||  | | |     |   ||   | |  || |  | |  || ||||||| ||||| |||||||| || |||||||| || ||||||||||| |||||||| |||||||  |||||||| |||||
gtaatagatatctatatatatctgtgtgtgtgtgtgtgtgtgtg-tgtgtaaactgttgttgggttaattaaattatattcctgcatttgattagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAATGCTTTAGCATTCAACCCTGATGGAAAGAG

upper sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S28_21V6.2 (Physcomitrella patens), 3'ss of exon 1
-----------gttagtgttgcagtaaaacagttttatttaaaaacttgtaa--cctggaaagagatatgtaactgtgtatttggtcttataatatat-agATTCTGCAAGAGGAAATTGGTGGCGTGAAAGGTCATTTTGGACCTATTAATGCTTTGGCATTCAGTCCTGATGGGAAGAG
              | |  | |   | |    |   |      ||||  |||  | | ||||||||    | | |     | | ||  | | |  |   ||||| |  |||||||||||||||| ||||| || ||||||||||||||||||||| | |  || | |||||| || | |||
aatgcctttttaccatttatccgagatattcatcacagactgcaactcataaagcatagaaagagaatccttatttaccgtctcgtgat-tgacgtgccagATTTTCGAAGAGGAAATTGGTGGTGTGAAGGGCCATTTTGGACCTATTAATGCTCTAGTTTTTAATCCTGACGGAAGGAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|116426847|gb|EG469439.1|EG469439
EST:     CTACCACTGATCATCGTGCTGGGAAGTTTGAAGCTAAGTTTTACGACACG                         ATTCTGCAAGAGGAAATTGGTGG
genomic: CTACCACTGATCATCGTGCTGGGAAGTTTGAAGCTAAGTTTTACGACACGgttagtgttg ... taatatatagATTCTGCAAGAGGAAATTGGTGG
EST: gi|116426850|gb|EG469442.1|EG469442
EST:     CTACCACTGATCATCGTGCTGGGAAGTTTGAAGCTAAGTTTTACGACACG                         ATTCTGCAAGAGGAAATTGGTGG
genomic: CTACCACTGATCATCGTGCTGGGAAGTTTGAAGCTAAGTTTTACGACACGgttagtgttg ... taatatatagATTCTGCAAGAGGAAATTGGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacttgtaacctggaaagagatatgtaactgtgtatttggtcttataatatatagATTCTGCAAGAGGAAATTGGTGGCGTGAAAGGTCATTTTGGACCTATTAATGCTTTGGCATTCAGTCCTGATGGGAAGAG
                                 tatttggtcttataat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgttgcagtaaaacagttttatttaaaaacttgtaacctggaaagagatatgtaactgtgtatttggtcttataatatatagATTCTGCAAGAGGAAATTGGTGGCGTGAAAGGTCATTTTGGACCTATTAATGCTTTGGCATTCAGTCCTGATGGGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA